[gmx-users] Adsorption energy of a single molecule

[Darrell Koskinen]

Hi Justin,
Thanks for the suggestion. I looked through the GROMACS manual and the 
only method I can see of obtaining the adsorption energy between an 
adsorbed ammonia molecule and the graphene sheet would be to create an 
index file that assigns a separate index for each ammonia molecule, run 
the simulation, and then run "gmxdump -e mdener.edr" to view the energy 
between the adsorbed ammonia molecule and the graphene sheet. Is this 
the method you are suggesting or is there a different method of 
obtaining this information?

Thanks.

Darrell
> Date: Thu, 29 Oct 2009 14:06:27 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Adsorption energy of a single molecule
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4AE9D9A3.9080004 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
> darrellk at ece.ubc.ca wrote:
>   
>> Dear GROMACS Gurus,
>> Is it possible to determine the adsorption energy of a single molecule in
>> a simulation? My simulation has a large number of gas phase molecules
>> distributed throughout a box with some molecules adsorbed on a graphene
>> sheet. I would like to compare the adsorption energy of a single
>> molecule to that reported in research papers.
>>
>>     
>
> You should be able to study interactions between individual molecules by using 
> energygrps and an appropriate index file.
>
> -Justin
>
>   
>> Thanks.
>>
>> Darrell
>>